ANGSD: Analysis of next generation Sequencing Data
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Abbababa: Difference between revisions
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[sequence data]->doAbbababa[ABBA and BABA couts file{bg:blue}] | [sequence data]->doAbbababa[ABBA and BABA couts file{bg:blue}] | ||
[ABBA and BABA couts file{bg:blue}]->jackKnife.R[D stat and Z scores{bg:blue}] | [ABBA and BABA couts file{bg:blue}]->jackKnife.R[D stat and Z scores{bg:blue}] | ||
</classdiagram> | |||
=Brief Overview= | =Brief Overview= | ||
<pre> | <pre> | ||
> ./angsd - | > ./angsd -doAbbababa | ||
-------------- | -------------- | ||
analysisAbbababa.cpp: | |||
- | -doAbbababa 0 | ||
1: use a random base | 1: use a random base | ||
-rmTrans 0 remove transitions | |||
-blockSize 5000000 number of based in a block | |||
- | |||
</pre> | </pre> | ||
This function will | This function will counts the number of ABBA and BABA sites | ||
=Options= | =Options= | ||
;-doFasta 1: sample a random base at each position. | ;-doFasta 1: sample a random base at each position. | ||
;-minQ [INT] | ;-minQ [INT] | ||
Revision as of 15:11, 2 December 2013
Available from version 0.559+.
performs the abbababa test also called the D-statistic. This tests for ancient admixture (or wrong tree topology)
<classdiagram type="dir:LR">
[Single BAM file{bg:orange}]->[Sequence data|Random base (-doAbbababa 1)]
[sequence data]->doAbbababa[ABBA and BABA couts file{bg:blue}] [ABBA and BABA couts file{bg:blue}]->jackKnife.R[D stat and Z scores{bg:blue}] </classdiagram>
Brief Overview
> ./angsd -doAbbababa -------------- analysisAbbababa.cpp: -doAbbababa 0 1: use a random base -rmTrans 0 remove transitions -blockSize 5000000 number of based in a block
This function will counts the number of ABBA and BABA sites
Options
- -doFasta 1
- sample a random base at each position.
- -minQ [INT]
minimum base quality score.
Output
Output is a fasta file, a normal looking fast file. Nothing special about this. For -doFasta 1, sometimes its big letters sometime small letters. This is due to the results being copied directly from the sequencing data. So small/big letters correspond to which strand for the original data. For the consensus fasta all letters are capital letters.
Example
Create a fasta file bases from a random samples of bases.
./angsd -i smallNA07056.mapped.ILLUMINA.bwa.CEU.low_coverage.20111114.bam -doFasta 1